vfdb ci

gbouras13 · Aug 23, 2023 · 615e4a0 · 615e4a0
1 parent 274159e
commit 615e4a0
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Showing 7 changed files with 229 additions and 24 deletions.
diff --git a/bin/input_commands.py b/bin/input_commands.py
@@ -216,20 +216,20 @@ def validate_meta(filepath_in, meta, split):
     if meta == True:
         if num_fastas < 2:
             logger.error(
-                "ERROR: -m meta mode specified when the input file only contains 1 contig. Please re-run without specifying -m. \n"
+                "ERROR: -m meta mode specified when the input file only contains 1 contig. Please re-run without specifying -m."
             )
         else:
             message = f"{num_fastas} input contigs detected."
             logger.info(message)
             if split == True:
-                message = "Split mode activtated. \nSeparate output FASTA, gff and genbank files will be output for each contig."
+                message = "Split mode activtated. Separate output FASTA, gff and genbank files will be output for each contig."
                 logger.info(message)
     else:
         if num_fastas > 1:
-            message = "More than one contig detected in the input file. Re-running pharokka with -m meta mode is recommended unless this is a fragmented isolate genome. \nContinuing."
+            message = "More than one contig detected in the input file. Re-running pharokka with -m meta mode is recommended unless this is a fragmented isolate genome. Continuing."
             logger.info(message)
         if split == True:
-            message = "-s or --split was specified without -m or --meta and will be ignored. \nPlease specify -s with -m if you want to run split mode. \nContinuing."
+            message = "-s or --split was specified without -m or --meta and will be ignored. Please specify -s with -m if you want to run split mode. Continuing."
             logger.info(message)
 
 

diff --git a/bin/pharokka.py b/bin/pharokka.py
@@ -287,24 +287,24 @@ def main():
     # running mmseqs2 on the 3 databases
     if mmseqs_flag is True:
         logger.info("Starting MMseqs2.")
-        run_mmseqs(
-            db_dir,
-            out_dir,
-            args.threads,
-            logdir,
-            gene_predictor,
-            args.evalue,
-            db_name="PHROG",
-        )
-        run_mmseqs(
-            db_dir,
-            out_dir,
-            args.threads,
-            logdir,
-            gene_predictor,
-            args.evalue,
-            db_name="CARD",
-        )
+        # run_mmseqs(
+        #     db_dir,
+        #     out_dir,
+        #     args.threads,
+        #     logdir,
+        #     gene_predictor,
+        #     args.evalue,
+        #     db_name="PHROG",
+        # )
+        # run_mmseqs(
+        #     db_dir,
+        #     out_dir,
+        #     args.threads,
+        #     logdir,
+        #     gene_predictor,
+        #     args.evalue,
+        #     db_name="CARD",
+        # )
         run_mmseqs(
             db_dir,
             out_dir,
@@ -317,7 +317,7 @@ def main():
 
     if hmm_flag is True:
         # runs pyhmmer on PHROGs
-        logger.info("Running PyHMMER .")
+        logger.info("Running PyHMMER on PHROGs.")
         best_results_pyhmmer = run_pyhmmer(
             db_dir, out_dir, args.threads, gene_predictor, args.evalue
         )

diff --git a/bin/post_processing.py b/bin/post_processing.py
@@ -2152,7 +2152,7 @@ def process_custom_pyhmmer_results(merged_df, custom_pyhmmer_results_dict):
             )
             merged_df.at[index, "custom_hmm_evalue"] = custom_pyhmmer_results_dict[
                 row["temp_prot"]
-            ].custom_hmm_evalue
+            ].evalue
 
     # drop temp prot
     merged_df = merged_df.drop(columns=["temp_prot"])

diff --git a/tests/run_overall.sh b/tests/run_overall.sh
@@ -37,6 +37,9 @@ pharokka.py -i $test_data/Standard_examples/SAOMS1.fasta -d $db_dir -o $out_dir/
 # mmseqs2_only
 pharokka.py -i $test_data/Standard_examples/SAOMS1.fasta -d $db_dir -o $out_dir/SAOMS1_mmseqs2_only -t 8 -f --mmseqs2_only
 
+# normal
+pharokka.py -i $test_data/custom_examples/MH649026.fasta -d $db_dir -o $out_dir/MH649026 -t 8 -f
+
 # meta
 pharokka.py -i $test_data/Meta_example/fake_meta.fa -d $db_dir -o $out_dir/fake_meta -t 8 -f -m
 

diff --git a/tests/test_data/custom_db/microvirus.h3m b/tests/test_data/custom_db/microvirus.h3m
diff --git a/tests/test_data/overall/custom_examples/MH649026.fasta b/tests/test_data/overall/custom_examples/MH649026.fasta
@@ -0,0 +1,2 @@
+>Family1_MH649026
+ATGAATAGGAACCTTGTTGATCTAACCAACTTGGCCTTTGGATCTGGTTATGTTGGTCGGTTGTGCGCTCTGAATGTGTTGCCGGTTGTTGCTGGTGACTCGATGGCCCTGGATGGGTACGTCAATCTTCGGTTGACTCCGTTTCTTCGTCAGCTGAATACTGACGTTAAAATCGACGTTTGTTCGTTCTACGTGCCTCATCGTCATATCTATGGGCAAGACTGGATCGATTTCATTAAGCAGGGCGTGGATGAGACGGTCACTTTCCCCACGGTTGCAGCTGCCAATCCGTACGGTGCCATGCACGCCATTCCCTGGACACATAATCGTGAGATGCCTTTGTGGCTTGTGCAGGGCTATCTCAATATTTGGAATAGGTATTATCGGCCGCCCCGCTCGGACATTGCGGAGCGGGTTATTGCTGACGGCTTGACGTCGTTTGACCAGTACGGTTTACGTTGTGCCAATCTCCCGGCCATCTGGAATACGGGCCACAAGGTTGCTGATTATCCGTCTGATGACACGGTCCCGTCGGCTACGACGTTTCGGCTCACTGAGATGGCCCGTGAGGCCGGTGAGTGGGAGTCTCGTCTGAACCGCGAATGGAAGGATAATTATTACTCTGACTTCATGAGGAATTCATTTGGTACGAGTATTAATACTGATGCTGACCAGCGGCCGTTGATGTTGGCCCATACGTCGGAGTGGGTTTCCGGTTTTGACGTTTATGGCACGTCCGGTGCGGCGTTTGGTGAGGCTCTCGGTCGCGCCCAAGCGTTGGTTCAGCATGGGTTTCCTCGCAGGATGTTTCCTGAGCATGGCGCAATTTGGACCCTTGCGTTGGTCCGTTACCCTTCCACCCACGAGAATGAGATCCATTATTTAGCTAGCAAGCCCCAGCCAACCTATGCGCAGATTGCGTCCGATCCTGCTGTTGATTCGGTGATTCCCCCAGCCGGCGTTATCGCCAGTGACTTGTTTCGGACTACCTCGGCTGCGGACCTGGGAATTATTCCCCATGGTCAGTGGTACCGGACTCAGCCTAATATCGTTCATAATAAGTATAACGAAATTAACGGGTTTGCGTTTCATAACCGGGTCCCGACTTCGTTGTCTGATGCGGTGCTTGGTGACACTGCAAGTATCACTCCTGCTTTCAAGAGTGCGGCAATGCTTCATTGGCAGACTTCTTCACGGTTCAACGTGAAGTGCCTGCGGGTTAGTGCTTCTTCTGGATCTTCTGTCTACGCTGGGACGAAACTTTAGTATTAATACTTCTTATTTTTATGAATGCTCCTACTGGTTTAGGTTACCCTCGCGATACGTTTAATGATGCTATTTGGGCGCCTACTACCTTTCCGGTGACTGGTGCCGGTGTGTCTACTCCGTTTCTTTGTCTTCCCGATGCTGCTTTGACTGGCACGGAGGAGCGGACTATTTTAGGTAATTTCCTATCCACGCTTTCGCTTGCTGCGAACACGAGGTCGGGATTTGGTATCGCGATTGGCGGTAATCGTCTTGGTCTTGAGGATGATGTTGCGGTGTATTTGCGGTACCAGCTGGATTATTCTTTCGAAGTTCCATATACTTCCGGCGGTACGGCCGGTGAGTTCCTGAAATTCCGGCCCGTGATCATTCGTAGGAATGTGAGTTTGTCTGGTGCCAATGTTTTTGTGGATTCGACCAACGCTATGGTGCCTCCTAATTCTAGGAGCCAGTGGGATGCTAGTTTGTCCAATAGTCTTGTTACTGATTTTTATCGCGTTTCCGGTTCTGCCTCTGGTGTTTTGGCGGTTTTTGGAACCGGCATCTATGCTGGTGAGAATCTCAGCTGTGGTCTGACGTTTTCTAACTCGAACACGTTTACCGGTTATGTTCGTGCCTTGTACATGTCGGTTGGTCTTAAATTCTGGACTTCCGATCAGCTTGCGCTGAATCCGAACGTGTGATGTTTGGTCTGCTTGCTGCTGGTGCTGCTTCTGGTGTTGCTGGTGGGGCTGCCAGTGGCCTGATGGGTTCGTCTGGCCCTGCTGCCCCTGCTGCTCCCCCTAGCTTTATGTCTGATGTTGGCTCTTCTTTGAAGGATGGCGTTGCTAGTGGTATTGGTTCTATTCCTGGACAGGCGCTTCAGGCTTCTGTAGGTTCTCGCATGGCCGGTAGGGCTCATCGGAATTTTCAGGACGGCGCTTTTCCGGGCACGACTCCGTTTGATCGTCTTTCGGGTTCTAATGGGTCCTCCGGTTCTTCCGGCGGCCCTTCTGATGCGGTGCGTGTAGCTAAGATTAACGCCCATGCTTCTGAGAGGGTCGCCCGTATTAATTCGACTGCACCTTTATCTCGTGAGAATCGTGAGGCTTCTGCCGGGACTGCTTCCGCTCAGGCGCTGAATTTGCGTTCTCAGGCTTCCCTTAATTCCACCCGGCGGCTTCTCGAACAAGCCAAGCTCCCTCGAGCTGTTCTCAATTCTAAGGCTGCTTCTGATTTTGCTGCCGCAGATCTAACTGAGGCGCAATCTAAGTCTATTGTGAATGCTACCGCTAATTTGATCCGCCGTGCTGGTGGTGCTTCTCCTGAGTCCGTTGCTAAGGGTCTTAGTCATTATGGTGATGCTATCGCTGAGCGTGTTTTATCTCTGTACCGTGCTTTTCTAGACGATTCTTCTTCTGTTCGTCGTCGTCTTCCTCGTCTTCCGGATTTTAAAAATACCAAGTGATTGGTTTTTATTTTGTTTTTGCTACTGGTCTACCACTTACATTCGGAGAGTTGACGTGATGCGCATCGCATCGGGTTGACGATACGAATCCTTGCTCTTATTTAACTTAATCGTGCTTTTGTTATGTATGTTTGCCGTTCTTCTGTTGATTTTGGTCTTACTGAGTTTGCTGTTTCTAAGCACTCCCGCTTGATTCGTAGTCTTGTTGTCGCTCGGAATCGTCTCTCTTCTCGTTTCTCTTCTAAGGCCCCTCCGGAGGGCCGTTCTATGGCTTCTCATCGTGCTGGTGTGGCCTTTCTGCGTTCTATTCAGGGGATTTTCGGTCGACTTGATAATCTATCCCTTATTACAGTGCCGTCGGTCTACGCGGCACTGTACAAGGAGGCCCAGCCAATCCTTTCTTTTGTTCGTCATGACCAGGGATCTCACGGGATCCGTGTTGAATGCGATGTGATTAAGCGAGTGCGCGAGACGCTCGTTCACAGCCGTAAGGCGGCACGGTTGTCTAGTTACCGTCGTAGGCTGAATAATGAGCTTAGAGAGGCTGCCAGGTATGATCGTTTCGTTGTGTTTAATACTGTTACCGTAAGGGATAGGGATTATCGAAAGGTTTTTGTTAAGGGTTCCCGTTTTTGGAATATTTTTACCGAGAAGGTGAAGGGTGCCGTCCAGGATGCTGCCGAAGATGCCGGTAGTATGGATACTTCTTATTTTGCCCACTTTGGCGTTGTTGAGGAGGGCTCTGAGACGGGCCGCCTTCATATACATTGCGTATGGGTTATGTCTCATTTGCCTCCTGGCTGCCGTGATCCGAATGGCGGTCGCGGCGGCGTCAATCGCGAGATTGATGCTCTTAGATCTCTGTGGCGTTTTGGGACGTCTACTCCCATTGCGGTGCGTTGGGCCAATGATCCCTATTCCCACTTGGGCTGGGTTTGGCCTTCGGTTCGAGTTAAGGACCTCGAGGGCAATTTTGTGTTGACTCCTGCCGTTTCGTCGCTAGAACGAATATGTTCATATCTCACCAAGTATATAACGAAGCCAAGTAAAACGTCGTGGAGAATTCGAATATCACACCGGTTCGGCCTTCGGGAGATAACCTCCCGCCTTCAGAAATTACCCCTGAAAACCCTAATAGCCCTGGCCAGCCTGTGGCCCCCGCGCTTGATGCCGGGGTTCCCGTTGGTCCGGAGGGCGGCAGTCCGCCTAGCGGCTTTGAGGATATTCCAGCAGTCGAGCGCTACCTTTTCGGATCATCAGATGGTGAACCAATTTTTGCTCATGTTGACTCCCAGGGAGAGTCTCTTCCACCGGTTGAAGAGGTTGGCTTTGAACATACCGGCTTCCACCCCAGCGAGTCCTGGGAGCTTAACGTTAACCTCGGACCCCGGGAGTGTATCTGATGCCCTGTCGTTCGTTGGAGAGCTCCGTGAGTTTTATGGAGAGAGATGTGACCTCGTCGGGTCTGTTTTCCTCGAGTGATTTTGAGGAACTTTTTTCTGAGTTGTGTGCTTTTGCTAGTTTGTTGGATGGTGGTGATTTTGCGACCAATCGGTTGCTGCTTGCTGCCTTGGCGCAATTTTTGTCTAGGAAACTTCGGATTCGCTTGGATGCGAATGCTGACATGTCCGTGCTTACTGATTTGATGGTTTTGACTAGGCAGACTTCTGTCGGTGCTTTTCCTTTGGAGGAGTATGAGGCGCACTTAACAGGTTTGCAGTTTTCTTTTGTATAGCTTATGGGCGATTTTCATATGATTAAAGGTGCCGTCAATGTCGTGCTGGCGTCTGGTTCGATTTACGCGGCGAATTTGACTGATGCCGATCTGGCCAGGGTTCGCGGAACCTCCCTTTGGCTCGCCGGAGACAGGATGAGGATGACAAGTGCTATGGATGTTTTGATGCAAGGATGCCTTCAGGTGGCAGGGATTCCCCCTTCCCAGTTGCCCTCTGAGGTCCGCGCGGCTGGCGTTGCTATGTTTGTGCATCCCGTTAACTGGATGACGGCGTGTGTCTGGCTTGGCGAGACCTACACGGTTGCCGCTGAGGCCCTTGGCGCCGAGGCTGGGCGCGGCCCTGTCCACGCTCAGCCTTTGCGACCTCGACAGCTCTACGCCTTGGTCCATGAGGCCTTTGGTGAAGCCGAGGGTTTCATGGCGAAATTTGTTAAACAGCTCGATGCCGTGACTTCTCCGATTAAGTTAAAATGATATGAAACACCGTTCAAAGTCTCGTTCGAAGCCTCGTTCCCGAAAGGGAAAGTATAAGGGTTCTACGTCGTCGTCTCGGCATACCGTGTCGCCTGGGACGGTTAAAGGCAACAAGCTTTGGTGGCGTGGCACTAATACGATTAT